Enrichment on steps, not genes, improves inference of differentially expressed pathways.
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ABSTRACT:
SUBMITTER: Markarian N
PROVIDER: S-EPMC10994554 | biostudies-literature | 2024 Mar
REPOSITORIES: biostudies-literature
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Enrichment on steps, not genes, improves inference of differentially expressed pathways.
Markarian Nicholas N Van Auken Kimberly M KM Ebert Dustin D Sternberg Paul W PW
PLoS computational biology 20240325 3
Enrichment analysis is frequently used in combination with differential expression data to investigate potential commonalities amongst lists of genes and generate hypotheses for further experiments. However, current enrichment analysis approaches on pathways ignore the functional relationships between genes in a pathway, particularly OR logic that occurs when a set of proteins can each individually perform the same step in a pathway. As a result, these approaches miss pathways with large or mult ...[more]
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| S-EPMC10078460 | biostudies-literature